Question: How to remove illumina PCR primer 2.01 from RNA-seq samples
1
gravatar for Grinch
4.0 years ago by
Grinch70
Germany
Grinch70 wrote:

I have RNA-seq samples that are highly contaminated with Illumina PCR primer 2.01, which programme is best to use to remove those?

 

 

rna-seq illumina • 2.7k views
ADD COMMENTlink modified 4.0 years ago by Juke-342.9k • written 4.0 years ago by Grinch70
2
gravatar for michael.ante
4.0 years ago by
michael.ante3.5k
Austria/Vienna
michael.ante3.5k wrote:

I'd recommend bbduck from the BBMap suite. It has included a lot of adapters and primer sequences, is very fast, and you can trim next to adapters also low-quality tails. Additionally, it is keeping your paired-end data in the correct order (if one read is removed, the other is removed too).

ADD COMMENTlink written 4.0 years ago by michael.ante3.5k
1

bbduk.sh (I make that mistake too). Adapters are in "adapters.fa" file in "resources" directory.

ADD REPLYlink written 4.0 years ago by genomax74k
2
gravatar for Benn
4.0 years ago by
Benn7.9k
Netherlands
Benn7.9k wrote:

Trim Galore worked for me.

http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

ADD COMMENTlink written 4.0 years ago by Benn7.9k
1
gravatar for Juke-34
4.0 years ago by
Juke-342.9k
Sweden
Juke-342.9k wrote:

cutadapt is also a nice one.

http://opensource.scilifelab.se/projects/cutadapt/

ADD COMMENTlink written 4.0 years ago by Juke-342.9k

To Juke-34. I have tried, but seems I could get the 3´primers cut off, I use the command cutadapt -a <reverse primer="" sequence=""> o <output name=""> directory/input file for the reverse primer sequence I hoped to cut, I tried the either the exact sequence of from 5´to 3´, or the reverse complementary one (the same as reverse primer as we order), both did not work. So any suggestions?

Thanks Ramona

ADD REPLYlink written 3.1 years ago by ramonaramonawan10

For reverse primer I guess the parameter is something like -A instead of -a. Did you read carefully the User Guide documentation ?
Everything is well explained with examples.

ADD REPLYlink written 3.0 years ago by Juke-342.9k
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